The Large Non-coding RNA ANRIL, which is Associated with Atherosclerosis, and Periodontitis, Trans-regulates ADIPOR1, VAMP3, and C11ORF10

The long non-coding RNA ANRIL (antisense lncRNA in the INK4 locus) is the best replicated genetic risk locus of coronary artery disease (CAD) and periodontitis, and independently associated with a variety of other immune-mediated and metabolic disorders, and several forms of cancer. How variants of this tissue specific and alternatively spliced lncRNA translate into different disease manifestations is currently unknown. Recent studies showed a correlation of decreased concentrations of proximal ANRIL transcripts with homozygous carriership of the CAD and periodontitis main risk alleles. To specifically target these isoforms, we constructed a short hairpin RNA in a stable inducible knock-down system of T-Rex 293 HEK cell-lines. By genome-wide expression profiling using Affymetrix HG1.0 ST Arrays, we identified the transcription of ADIPOR1, VAMP3, and C11ORF10 to be correlated with decreased ANRIL expression in a time-depending manner. We validated these findings on a transcriptional and translational level in different cell types. Additionally, exploration of the identified genes for the presence of variants associated with CAD and periodontitis, using Affymetrix 500K genotyping and Illumina custom genotyping arrays, highlighted a region upstream VAMP3 within CAMTA1 that was previously shown to be associated with a complex of periodontal pathogens, to be associated with increased risk of CAD (rs10864294 p=0.015, OR=1.30, 95% confidence interval [C.I.] =1.1-1.6, 1,471 cases, 2,737 healthy controls) and aggressive periodontitis (AgP; p=0.008, OR=1.31, 95% [C.I.=1.1-1.6], 864 cases, 3,664 matched controls). Our results give evidence that specific isoforms of ANRIL regulate key genes of glucose- and plasma fatty acid metabolism.